I've always read it as at least a little bit a comment on the Iraq war, but what's it's deal? It's the only anime I can think of that climaxes with a military coup, and its cool that mustang wants to put people on trial for war crimes, but then he gets in power and doesn't do it.
It's also just got a whole plotline about racism, but it feels slightly off? Like minorities are okay if they save your life.
Hideaki Anno has been saying similar stuff about his fans for decades now, yet most people are still saying
:so-true: cool robots and sexualized 14 year olds!
Same for Tomino's stuff [though at least he didn't really engage in sexualization of his characters].
Oshii mostly avoided this fate though, by being very mask off when he gets around to being political.